VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Sun Oct 15 2023 - 11:19:51 CDT

I believe that should be CG2O2, not CG202 (the letter O, not the number 0). It can be hard to tell sometimes!

Best,
JC

On Oct 15, 2023, at 12:01 PM, Joel Subach <mjsubach_at_alumni.ncsu.edu> wrote:

Hello Josh thank you for your kind update:).

I amended, as you had recommended, the .prm file generated during my initial ffTK run and precipitated the same error
(see screenshot attached labeled FATAL ERROR where at the top-right you can read the error and the bottom right
exhibits my modified .prm file as recommended, on the left is the OPT Torsion GUI. Also attached is the complete error-
log file for your inspection. Thanks if you can help:)

Best,
Joel 🚀

On Sat, Oct 14, 2023 at 7:15 PM Vermaas, Josh <vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>> wrote:
Hi Joel,

Take a look at par_all36m_prot.prm from the standard CHARMM parameter file. There will be an improper section that you can crib from. A typical line will look something like this:

HR1 NR1 NR2 CPH2 0.5000 0 0.0000

You'd change the 4 atomtypes to be what you need them to be for your system, and then make the 0.5 (the force constant for the improper energy) 0.

-Josh

On 10/14/23, 11:37 AM, "owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> <mailto:owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of Joel Subach" <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> <mailto:owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of mjsubach_at_alumni.ncsu.edu<mailto:mjsubach_at_alumni.ncsu.edu> <mailto:mjsubach_at_alumni.ncsu.edu<mailto:mjsubach_at_alumni.ncsu.edu>>> wrote:


Hello JC thank you so much for teaching me via your kind update:).


Can you please be more specific in this modification since I have never
done this before, below is my .par existing file:


IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!


i.e. how would you suggest to modify the above i.e. add the dummy improper
with a force constant of zero?


Thanks if you can:)
Joel 🚀


On Sat, Oct 14, 2023 at 4:49 AM Gumbart, JC <gumbart_at_physics.gatech.edu<mailto:gumbart_at_physics.gatech.edu> <mailto:gumbart_at_physics.gatech.edu<mailto:gumbart_at_physics.gatech.edu>>>
wrote:


> Hi Joel,
>
> You could just manually add a dummy improper with a force constant of zero
> for now. You can then optimize the improper after getting the dihedrals.
>
> Best,
> JC
>
> On Oct 13, 2023, at 7:52 AM, Joel Subach <mjsubach_at_alumni.ncsu.edu<mailto:mjsubach_at_alumni.ncsu.edu> <mailto:mjsubach_at_alumni.ncsu.edu<mailto:mjsubach_at_alumni.ncsu.edu>>> wrote:
>
> Hello VMD Community, towards the above topic:
>
> Via the ffTK Opt Torsions Tab to optimize dihedral parameters (Tutorial 6.2
> link: *https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$ <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$>
> <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$ <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$> >).*
>
> I had clicked Run Optimization after inputting:
>
> all of the proper files i.e. psf, pdb, par for the *input section *
>
> my 4-output.out resulting files generated via ORCA for the *QM Target
> Data Section*
>
> and my atom types for my two-dihedral angles for the *Dihedral Parameter
> Settings*
>
> the below error states:
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51 OG2D1
> OG311 (ATOMS 17 7 37 36)
> [Partition 0][Node 0] End of program
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51 OG2D1
> OG311 (ATOMS 17 7 37 36)
>
> (See complete Application_Error.log file attached and note within it the: *Info:
> 0 IMPROPER*
> may have been generated via ffTK?)
>
> Below is a paste of the impropers from my generated .par file:
>
> IMPROPER
> !
> !V(improper) = Kpsi(psi - psi0)**2
> !
> !Kpsi: kcal/mole/rad**2
> !psi0: degrees
> !note that the second column of numbers (0) is ignored
> !
> !atom types Kpsi psi0
> !
>
> * Note i skipped to Scan Torsions since that was all I needed amended i.e

<FATAL_ERROR.png><SAVE_TO_LOG.log>